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An R package for single-cell CRISPR screen data analysis emphasizing statistical rigor, massive scalability, and ease of use.

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sceptre

sceptre is an R package for single-cell CRISPR screen data analysis, emphasizing statistical rigor, massive scalability, and ease of use.

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v0.10.0: sceptre at massive scale

sceptre v0.10.0 represents another a major upgrade to the sceptre software. We have integrated sceptre with ondisc, a companion R package that facilitates large-scale computing on single-cell data. sceptre now supports the analysis of single-cell CRISPR screen data out-of-core on a laptop or distributed across hundreds of processors on a computing cluster or cloud.

sceptre v0.10.0 includes the following updates:

  • Support for disk-backed sceptre objects, enabling the analysis of data too large to fit in memory
  • A sceptre Nextflow pipeline, enabling the deployment of sceptre across hundreds of processors on a cluster or cloud
  • An updated e-book containing new sections about at-scale sceptre and the statistical methodology underlying sceptre
  • New functionality for plotting and inspecting gRNA-to-cell assignments
  • A comprehensive suite of unit tests, which verify the correctness of the code
  • More detailed man pages (including runnable examples) and minor bug fixes

You can see our RECOMB poster for more information about this update.

Featured publications

sceptre also recently was featured in a 10x Genomics analysis guide.

Bug reports, feature requests, and software questions

For bug reports, please open a GitHub issue. For questions about sceptre functionality, documentation, or how to apply it to your data, please start a discussion under Q&A.

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An R package for single-cell CRISPR screen data analysis emphasizing statistical rigor, massive scalability, and ease of use.

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